This white paper presents an FPGA-based accelerated solution for DNA sequencing and dot plotting. It describes how multiple FPGA devices can be deployed to create a scalable cluster dedicated to the task of analyzing large amounts of data, and how this clustered hardware application can be connected to a software application for visualization and analysis.

Also discussed, parallel FPGA optimizations, and how higher-level programming methods, using the C language, can speed the development of this and other types of highly parallel algorithms.